diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index ebdad467ff61..45d276dd796b 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -3706,12 +3706,15 @@ void EditorNode::_remove_scene(int index, bool p_change_tab) {
 }
 
 void EditorNode::set_edited_scene(Node *p_scene) {
+	set_edited_scene_root(p_scene, true);
+}
+
+void EditorNode::set_edited_scene_root(Node *p_scene, bool p_auto_add) {
 	Node *old_edited_scene_root = get_editor_data().get_edited_scene_root();
-	if (old_edited_scene_root) {
-		if (old_edited_scene_root->get_parent() == scene_root) {
-			scene_root->remove_child(old_edited_scene_root);
-		}
-		old_edited_scene_root->disconnect(SNAME("replacing_by"), callable_mp(this, &EditorNode::set_edited_scene));
+	ERR_FAIL_COND_MSG(p_scene && p_scene != old_edited_scene_root && p_scene->get_parent(), "Non-null nodes that are set as edited scene should not have a parent node.");
+
+	if (p_auto_add && old_edited_scene_root && old_edited_scene_root->get_parent() == scene_root) {
+		scene_root->remove_child(old_edited_scene_root);
 	}
 	get_editor_data().set_edited_scene_root(p_scene);
 
@@ -3723,11 +3726,8 @@ void EditorNode::set_edited_scene(Node *p_scene) {
 		get_tree()->set_edited_scene_root(p_scene);
 	}
 
-	if (p_scene) {
-		if (p_scene->get_parent() != scene_root) {
-			scene_root->add_child(p_scene, true);
-		}
-		p_scene->connect(SNAME("replacing_by"), callable_mp(this, &EditorNode::set_edited_scene));
+	if (p_auto_add && p_scene) {
+		scene_root->add_child(p_scene, true);
 	}
 }
 
@@ -5967,6 +5967,8 @@ void EditorNode::reload_instances_with_path_in_edited_scenes(const String &p_ins
 						instantiated_node->set_scene_file_path(String());
 					}
 					current_edited_scene = instantiated_node;
+
+					editor_data.set_edited_scene_root(current_edited_scene);
 				}
 
 				// Replace the original node with the instantiated version.
diff --git a/editor/editor_node.h b/editor/editor_node.h
index 5d7bd5b4f812..899da9945013 100644
--- a/editor/editor_node.h
+++ b/editor/editor_node.h
@@ -783,6 +783,7 @@ public:
 	SubViewport *get_scene_root() { return scene_root; } // Root of the scene being edited.
 
 	void set_edited_scene(Node *p_scene);
+	void set_edited_scene_root(Node *p_scene, bool p_auto_add);
 	Node *get_edited_scene() { return editor_data.get_edited_scene_root(); }
 
 	void fix_dependencies(const String &p_for_file);
diff --git a/editor/scene_tree_dock.cpp b/editor/scene_tree_dock.cpp
index 2f57dc56101d..c71cb9d4ac96 100644
--- a/editor/scene_tree_dock.cpp
+++ b/editor/scene_tree_dock.cpp
@@ -2992,6 +2992,10 @@ void SceneTreeDock::_replace_node(Node *p_node, Node *p_by_node, bool p_keep_pro
 			to_erase.push_back(oldnode->get_child(i));
 		}
 	}
+
+	if (oldnode == edited_scene) {
+		EditorNode::get_singleton()->set_edited_scene_root(newnode, false);
+	}
 	oldnode->replace_by(newnode, true);
 
 	// Re-apply size of anchored control.